Software

This page lists the software projects our group is involved in. Most of the software is hosted at bioinfweb. You can find detailed user and developer documentations to most of the projects there, if you follow the links below. Additionally formal definitions of the XML formats used in our software is privided on BioInfWeb.

JTreeSS

JTreeSS icon
Project home:   http://bioinfweb.info/JTreeSS/
Current version:   (Jul 8, 2019 10:00:00 AM)
Developers / contributers:   Ben Stöver, Charlotte Schmitt

A library that reads and interprets style sheets for phylogenetic trees in the TreeSS format and can apply them to any data model representing a phylogenetic tree.

TreeGraph 2

TreeGraph 2 icon
Project home:   http://treegraph.bioinfweb.info/
Current version:   2.15.0 beta (Apr 26, 2019 8:35:00 PM)
Developers / contributers:   Ben Stöver, Sarah Wiechers, Kai Müller

TreeGraph 2 is a graphical editor for phylogenetic trees that features a variety of formatting options for the elements of a tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).

bioinfweb.commons.java

bioinfweb.commons.java icon
Project home:   http://commons.bioinfweb.info/Java/
Current version:   3.3.1 (Apr 26, 2019 7:10:00 PM)
Developers / contributers:   Ben Stöver, Sarah Wiechers

A Java library containing the shared components developed for different bioinfweb projects. These components are made publicly available under GNU LGPL 3.

PhyDE 2

PhyDE 2 icon
Project home:   http://bioinfweb.info/PhyDE2/
Current version:   0.0.0 alpha (May 15, 2018 12:00:00 PM)
Developers / contributers:   Ben Stöver, Jonas Bohn, Sarah van Groen, Lara Kösters, Dietmar Quandt, Kai Müller

A multiple sequence alignment editor for phylogenetic purposes based on the functionality of LibrAlign and JPhyloIO.

LibrAlign

LibrAlign icon
Project home:   http://bioinfweb.info/LibrAlign
Current version:   0.9.0 (Apr 18, 2018 5:37:00 PM)
Developers / contributers:   Ben Stöver, Kai Müller

LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data

AlignmentComparator

AlignmentComparator icon
Project home:   http://bioinfweb.info/AlignmentComparator
Current version:   1.0.0 beta (Mar 1, 2018 12:20:00 PM)
Developers / contributers:   Ben Stöver, Kai Müller

AlignmentComparator is a GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same data set.

TIC

TIC icon
Project home:   http://bioinfweb.info/TIC/
Current version:   3.0.2 (Feb 26, 2018 3:10:00 PM)
Developers / contributers:   Ben Stöver, Sarah Wiechers

Toolkit independent components (TIC) - A Java library for creating GUI components for Swing and SWT

GBOL5 web application

GBOL5 web application icon
Project home:   http://gbol5.de/
Current version:   0.0.1 (Mar 15, 2015 3:40:34 PM)
Developer:   Kai Müller

Ruby on Rails application for mass assembly of primer reads generated in the GBOL5 project into contigs, auto-assignment of reads to isolates, specimens, species and management of specimens, target species, etc.

PhyDE

PhyDE icon
Project home:   http://www.phyde.de/
Current version:   0.9951 (Mar 31, 2008 12:00:00 AM)
Developers / contributers:   Jörn Müller, Kai Müller, Dietmar Quandt

System-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data

GraphicMeasurer

GraphicMeasurer icon
Project home:   http://gm.bioinfweb.info/
Current version:   (Jan 2, 2007 1:53:11 PM)
Developers / contributers:   Ben Stöver, Horst Bleckmann

GraphicMeasurer is a program that is able to analyze graphics and videos by locating and tracking objects (e.g. moving animals). The extracted geometric objects can be referenced with a spread-sheet-like result sheet language which allows to generate tables containing positions, angles or more complex data derived from the located objects.

IndelCoder

IndelCoder icon
Project home:   http://bioinfweb.info/Software/IndelCoder
Current version:   0.5 (Aug 30, 2005 12:00:00 AM)
Developer:   Kai Müller

Automates encoding of indels according to 10 different schemes, including simple binary and complex matrix character schemes.

Note that IndelCoder is not available for download anymore, since all its functionality has been moved to SeqState.

PRAP

PRAP icon
Project home:   http://bioinfweb.info/Software/PRAP
Current version:   1.0 (Jul 12, 2005 12:00:00 AM)
Developer:   Kai Müller

Precursor of PRAP2. Parsimony ratchet analyses with PAUP* including random addition cycles of the ratchet and calculation of Bremer support applying the ratchet.